FEAST
This is the released version of FEAST; for the devel version, see FEAST.
FEAture SelcTion (FEAST) for Single-cell clustering
Bioconductor version: Release (3.23)
Cell clustering is one of the most important and commonly performed tasks in single-cell RNA sequencing (scRNA-seq) data analysis. An important step in cell clustering is to select a subset of genes (referred to as “features”), whose expression patterns will then be used for downstream clustering. A good set of features should include the ones that distinguish different cell types, and the quality of such set could have significant impact on the clustering accuracy. FEAST is an R library for selecting most representative features before performing the core of scRNA-seq clustering. It can be used as a plug-in for the etablished clustering algorithms such as SC3, TSCAN, SHARP, SIMLR, and Seurat. The core of FEAST algorithm includes three steps: 1. consensus clustering; 2. gene-level significance inference; 3. validation of an optimized feature set.
Author: Kenong Su [aut, cre], Hao Wu [aut]
Maintainer: Kenong Su <kenong.su at emory.edu>
citation("FEAST")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("FEAST")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("FEAST")| The FEAST User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, FeatureExtraction, Sequencing, SingleCell, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | GPL-2 |
| Depends | R (>= 4.1), mclust, BiocParallel, SummarizedExperiment |
| Imports | SingleCellExperiment, methods, stats, utils, irlba, TSCAN, SC3, matrixStats |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/suke18/FEAST/issues |
See More
| Suggests | rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0), BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | FEAST_1.20.0.tar.gz |
| Windows Binary (x86_64) | FEAST_1.20.0.zip |
| macOS Binary (big-sur-x86_64) | FEAST_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | FEAST_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/FEAST |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/FEAST |
| Bioc Package Browser | https://code.bioconductor.org/browse/FEAST/ |
| Package Short Url | https://bioconductor.org/packages/FEAST/ |
| Package Downloads Report | Download Stats |